I have written the program MinRMS, a tool for protein structure alignment designed to integrate into Chimera. MinRMS is the implementation of a structural alignment algorithm that produces multiple superpositions of two molecules. Each resulting superposition matches a different number of pairs of residues and has the lowest RMSD among all possible superpositions that match the same number of residue pairs. MinRMS is being used to examine structural similarity between members of superfamilies as well as to identify possible active sites when given a template site.